{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T13:20:04Z","timestamp":1787318404206,"version":"build-2736575974"},"reference-count":28,"publisher":"Cambridge University Press (CUP)","issue":"1","license":[{"start":{"date-parts":[[2023,3,8]],"date-time":"2023-03-08T00:00:00Z","timestamp":1678233600000},"content-version":"unspecified","delay-in-days":66,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["ASHE"],"published-print":{"date-parts":[[2023]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec id=\"S2732494X23001195_as1\">\n                    <jats:title>Objectives:<\/jats:title>\n                    <jats:p>We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"S2732494X23001195_as2\">\n                    <jats:title>Design and setting:<\/jats:title>\n                    <jats:p>This 18-month prospective molecular epidemiology study was conducted at a tertiary-care hospital in Montreal, Canada. When nosocomial transmission was suspected by local infection control, viral genomic sequencing was performed locally for all putative outbreak cases. Molecular and conventional epidemiology data were correlated on a just-in-time basis to improve understanding of coronavirus disease 2019 (COVID-19) transmission and reinforce or adapt control measures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"S2732494X23001195_as3\">\n                    <jats:title>Results:<\/jats:title>\n                    <jats:p>Between April 2020 and October 2021, 6 outbreaks including 59 nosocomial infections (per the epidemiological definition) were investigated. Genomic data supported 7 distinct transmission clusters involving 6 patients and 26 healthcare workers. We identified multiple distinct modes of transmission, which led to reinforcement and adaptation of infection control measures. Molecular epidemiology data also refuted (n = 14) suspected transmission events in favor of community acquired but institutionally clustered cases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"S2732494X23001195_as4\">\n                    <jats:title>Conclusion:<\/jats:title>\n                    <jats:p>SARS-CoV-2 genomic sequencing can refute or strengthen transmission hypotheses from conventional nosocomial epidemiological investigations, and guide implementation of setting-specific control strategies. Our study represents a template for prospective, on site, outbreak-focused SARS-CoV-2 sequencing. This approach may become increasingly relevant in a COVID-19 endemic state where systematic sequencing within centralized surveillance programs is not available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"S2732494X23001195_as5\">\n                    <jats:title>Trial registration:<\/jats:title>\n                    <jats:p>clinicaltrials.gov identifier: NCT05411562<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1017\/ash.2023.119","type":"journal-article","created":{"date-parts":[[2023,3,8]],"date-time":"2023-03-08T03:40:18Z","timestamp":1678246818000},"source":"Crossref","is-referenced-by-count":3,"title":["On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study"],"prefix":"10.1017","volume":"3","author":[{"given":"Patrick","family":"Benoit","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gis\u00e8le","family":"Jolicoeur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8757-2049","authenticated-orcid":false,"given":"Floriane","family":"Point","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chantal","family":"Soucy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Normand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Morency-Potvin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Gagnon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4467-136X","authenticated-orcid":false,"given":"Daniel E.","family":"Kaufmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3440-3436","authenticated-orcid":false,"given":"C\u00e9cile","family":"Tremblay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2025-8928","authenticated-orcid":false,"given":"Fran\u00e7ois","family":"Coutl\u00e9e","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. Richard","family":"Harrigan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Hardy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2259-1713","authenticated-orcid":false,"given":"Martin","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrice","family":"Savard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3646-1573","authenticated-orcid":false,"given":"Simon","family":"Grandjean Lapierre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2023,3,8]]},"reference":[{"key":"S2732494X23001195_ref13","article-title":"Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore","author":"Tyson","year":"2020","journal-title":"bioRxiv"},{"key":"S2732494X23001195_ref28","doi-asserted-by":"crossref","first-page":"vex042","DOI":"10.1093\/ve\/vex042","article-title":"TreeTime: maximum-likelihood phylodynamic analysis","volume":"4","author":"Sagulenko","year":"2018","journal-title":"Virus Evol"},{"key":"S2732494X23001195_ref2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejca.2020.08.017"},{"key":"S2732494X23001195_ref21","first-page":"13","article-title":"Nosocomial outbreak of SARS-CoV-2 in a \u201cnon\u2013COVID-19\u201d hospital ward: virus genome sequencing as a key tool to understand cryptic transmission","author":"Borges","year":"2021","journal-title":"Viruses"},{"key":"S2732494X23001195_ref8","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(20)30527-2"},{"key":"S2732494X23001195_ref15","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-86265-4"},{"key":"S2732494X23001195_ref3","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(20)31182-X"},{"key":"S2732494X23001195_ref11","doi-asserted-by":"publisher","DOI":"10.1017\/ice.2020.1420"},{"key":"S2732494X23001195_ref19","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhin.2021.02.005"},{"key":"S2732494X23001195_ref5","unstructured":"5. Prevention, identification, and management of health worker infection in the context of COVID-19. Interim guidance. World Health Organization website. https:\/\/www.who.int\/publications-detail-redirect\/10665-336265. Published October 30, 2020. 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World Health Organization website. https:\/\/www.who.int\/publications\/i\/item\/9789240018440. Published 2021. Accessed February 14, 2023."},{"key":"S2732494X23001195_ref14","unstructured":"14. Loman, N , Rowe, W , Rambaut, A. ARTIC-nCoV-bioinformaticsSOP-v1.1.0. ARCTICnetwork website. https:\/\/artic.network\/ncov-2019\/ncov2019-bioinformatics-sop.html. Published 2020. Accessed June 12, 2020, 2020."},{"key":"S2732494X23001195_ref4","unstructured":"4. Interim infection prevention and control recommendations for healthcare personnel during the coronavirus disease 2019 (COVID-19) pandemic. Centers for Disease Control and Prevention website. https:\/\/www.cdc.gov\/coronavirus\/2019-ncov\/hcp\/infection-control-recommendations.html. Published 2021. Accessed February 14, 2023."},{"key":"S2732494X23001195_ref6","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13756-020-00875-7","article-title":"Nosocomial transmission and outbreaks of coronavirus disease 2019: the need to protect both patients and healthcare workers","volume":"10","author":"Abbas","year":"2021","journal-title":"Antimicrob Resist Infect Control"},{"key":"S2732494X23001195_ref10","doi-asserted-by":"publisher","DOI":"10.1016\/j.puhe.2021.03.011"},{"key":"S2732494X23001195_ref12","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2020.104615"},{"key":"S2732494X23001195_ref24","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2021.145496"},{"key":"S2732494X23001195_ref9","unstructured":"9. SARS-CoV-2: Mesures de pr\u00e9vention et contr\u00f4le des infections pour les milieux de soins de courte dur\u00e9e. Institut national de sant\u00e9 publique du Qu\u00e9bec website. https:\/\/www.inspq.qc.ca\/publications\/2906-pci-soins-aigus-covid19. 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